Functional annotation of the 2q35 breast cancer risk locus implicates a structural variant in influencing activity of a long-range enhancer element.
Baxter JS., Johnson N., Tomczyk K., Gillespie A., Maguire S., Brough R., Fachal L., Michailidou K., Bolla MK., Wang Q., Dennis J., Ahearn TU., Andrulis IL., Anton-Culver H., Antonenkova NN., Arndt V., Aronson KJ., Augustinsson A., Becher H., Beckmann MW., Behrens S., Benitez J., Bermisheva M., Bogdanova NV., Bojesen SE., Brenner H., Brucker SY., Cai Q., Campa D., Canzian F., Castelao JE., Chan TL., Chang-Claude J., Chanock SJ., Chenevix-Trench G., Choi J-Y., Clarke CL., NBCS Collaborators None., Colonna S., Conroy DM., Couch FJ., Cox A., Cross SS., Czene K., Daly MB., Devilee P., Dörk T., Dossus L., Dwek M., Eccles DM., Ekici AB., Eliassen AH., Engel C., Fasching PA., Figueroa J., Flyger H., Gago-Dominguez M., Gao C., García-Closas M., García-Sáenz JA., Ghoussaini M., Giles GG., Goldberg MS., González-Neira A., Guénel P., Gündert M., Haeberle L., Hahnen E., Haiman CA., Hall P., Hamann U., Hartman M., Hatse S., Hauke J., Hollestelle A., Hoppe R., Hopper JL., Hou M-F., kConFab Investigators None., ABCTB Investigators None., Ito H., Iwasaki M., Jager A., Jakubowska A., Janni W., John EM., Joseph V., Jung A., Kaaks R., Kang D., Keeman R., Khusnutdinova E., Kim S-W., Kosma V-M., Kraft P., Kristensen VN., Kubelka-Sabit K., Kurian AW., Kwong A., Lacey JV., Lambrechts D., Larson NL., Larsson SC., Le Marchand L., Lejbkowicz F., Li J., Long J., Lophatananon A., Lubiński J., Mannermaa A., Manoochehri M., Manoukian S., Margolin S., Matsuo K., Mavroudis D., Mayes R., Menon U., Milne RL., Mohd Taib NA., Muir K., Muranen TA., Murphy RA., Nevanlinna H., O'Brien KM., Offit K., Olson JE., Olsson H., Park SK., Park-Simon T-W., Patel AV., Peterlongo P., Peto J., Plaseska-Karanfilska D., Presneau N., Pylkäs K., Rack B., Rennert G., Romero A., Ruebner M., Rüdiger T., Saloustros E., Sandler DP., Sawyer EJ., Schmidt MK., Schmutzler RK., Schneeweiss A., Schoemaker MJ., Shah M., Shen C-Y., Shu X-O., Simard J., Southey MC., Stone J., Surowy H., Swerdlow AJ., Tamimi RM., Tapper WJ., Taylor JA., Teo SH., Teras LR., Terry MB., Toland AE., Tomlinson I., Truong T., Tseng C-C., Untch M., Vachon CM., van den Ouweland AMW., Wang SS., Weinberg CR., Wendt C., Winham SJ., Winqvist R., Wolk A., Wu AH., Yamaji T., Zheng W., Ziogas A., Pharoah PDP., Dunning AM., Easton DF., Pettitt SJ., Lord CJ., Haider S., Orr N., Fletcher O.
A combination of genetic and functional approaches has identified three independent breast cancer risk loci at 2q35. A recent fine-scale mapping analysis to refine these associations resulted in 1 (signal 1), 5 (signal 2), and 42 (signal 3) credible causal variants at these loci. We used publicly available in silico DNase I and ChIP-seq data with in vitro reporter gene and CRISPR assays to annotate signals 2 and 3. We identified putative regulatory elements that enhanced cell-type-specific transcription from the IGFBP5 promoter at both signals (30- to 40-fold increased expression by the putative regulatory element at signal 2, 2- to 3-fold by the putative regulatory element at signal 3). We further identified one of the five credible causal variants at signal 2, a 1.4 kb deletion (esv3594306), as the likely causal variant; the deletion allele of this variant was associated with an average additional increase in IGFBP5 expression of 1.3-fold (MCF-7) and 2.2-fold (T-47D). We propose a model in which the deletion allele of esv3594306 juxtaposes two transcription factor binding regions (annotated by estrogen receptor alpha ChIP-seq peaks) to generate a single extended regulatory element. This regulatory element increases cell-type-specific expression of the tumor suppressor gene IGFBP5 and, thereby, reduces risk of estrogen receptor-positive breast cancer (odds ratio = 0.77, 95% CI 0.74-0.81, p = 3.1 × 10-31).